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Sample GSM361434

Query DataSets for GSM361434

Status

Public on Jan 17, 2009

Title

MBcells_Ptc+-_Ink4c--_rep4

Sample type

SRA

Source name

Purified GNP-like medulloblastoma cells from cerebellum

Organism

Mus musculus

Characteristics

Ptch1+/-, Ink4c (p18) -/-
genotype: Ptch1+/-, Ink4c (p18) -/-; Tissue: MB cells; Age: variable

Growth protocol

Standard mouse facility

Extracted molecule

total RNA

Extraction protocol

Total RNA extraction by Trizol

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina Genome Analyzer

Description

Barcode used in pool: 5MLB
Raw data file: CSHL_FC11273_8_Medullo_6.fastq

Data processing

The reads were deconvoluted by barcode, collapsed to unique sequences, aligned to the genome and annotated. Read-counts for miRNA sequences were cubic-spline normalized then log-transformed. The R-project software (http://www.R-project.org), including Bioconductor were used for data analysis.

Submission date

Jan 16, 2009

Last update date

Mar 04, 2023

Contact name

Fedor Karginov

E-mail(s)

karginov@ucr.edu

Organization name

UC Riverside

Department

MCSB

Street address

900 University Ave

City

Riverside

State/province

California

ZIP/Postal code

92521

Country

USA

Platform ID

GPL9185

Series (1)

GSE14470

MicroRNA profiling in mouse medulloblastomas and normal cerebellar tissues

Relations

BioSample

SAMN02195496

Data table header descriptions
SEQUENCE
COUNT	Read-counts for miRNA sequences were cubic-spline normalized then log-transformed

Data table
SEQUENCE	COUNT
mmu-let-7a (main)	3.041655246
mmu-let-7a (other)	0.068601136
mmu-let-7b (main)	3.295293272
mmu-let-7b (other)	0.320394014
mmu-let-7c (main)	3.857732262
mmu-let-7c (other)	0.453140674
mmu-let-7c$mmu-let-7a (main)	0.453140674
mmu-let-7c$mmu-let-7a (other)	0.068601136
mmu-let-7c$mmu-let-7a$mmu-let-7c$mmu-let-7a (main)	1.398752127
mmu-let-7d (main)	2.709750693
mmu-let-7d (other)	1.2434052
mmu-let-7e (main)	2.04852831
mmu-let-7e (other)	0.068601136
mmu-let-7f (main)	3.148740108
mmu-let-7f (other)	0.068601136
mmu-let-7g (main)	2.900722351
mmu-let-7g (other)	0.068601136
mmu-let-7i (main)	2.388221249
mmu-let-7i (other)	0.068601136
mmu-mir-1 (main)	0.320394014

Total number of rows: 528

Table truncated, full table size 16 Kbytes.

Supplementary data files not provided

Processed data included within Sample table